8IZS | pdb_00008izs

Structure of a triple-helix region of human collagen type XVII

PDB DOI: https://doi.org/10.2210/pdb8IZS/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2023-04-07 Released: 2024-10-16
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.242 (Depositor), 0.234 (DCC)
R-Value Work:
0.206 (Depositor), 0.202 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of a triple-helix region of human collagen type XVII

Zhu, Y., Yang, X., Sun, F.

To be published.

Macromolecule Content

Total Structure Weight: 15.02 kDa
Atom Count: 1,310
Modeled Residue Count: 165
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(XVII) chain	A, B, C, D, E A, B, C, D, E, F	28	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMD9 (Homo sapiens) Explore Q9UMD9 Go to UniProtKB: Q9UMD9
PHAROS: Q9UMD9 GTEx: ENSG00000065618
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UMD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.242 (Depositor), 0.234 (DCC)
R-Value Work: 0.206 (Depositor), 0.202 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.38	α = 78.4
b = 30.05	β = 78.12
c = 40.12	γ = 64.27

Software Package:

Software Name	Purpose
PHENIX	refinement
pointless	data scaling
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.